Subscribe to receive announcements about upcoming Bioinformatics Seminars with this procedure:

• Send a plain-text e-mail to listproc@ku.edu. Your e-mail should contain the following single line of text in the message body (the subject line does not matter):
  SUBSCRIBE bioinfo Your Name
  
  The list server will send you back a confirmation.
• If the above fails for some reason, please send an e-mail to David Johnson habib@ittc.ku.edu

Please, note the location for each seminar, as it may be different from one event to another.

We welcome prospective speakers. If you want to become a speaker at the Seminar, please, e-mail or call our seminar coordinator from the Contact page.

• 2013 Spring Semester

  
  5/14 Dr. David Kristensen (Evolutionary Genomics Research Group, NIH)
  Bioinformatics applications to study bacteriophage-host interactions in human intestines and elsewhere
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  dk131363@gmail.com
  
  4/25 Dr. Alex Sodt (Laboratory of Computational Biology, NIH)
  Modeling how membrane mechanical properties couple to protein function
  Time: 3:00 pm
  Location: MRB 200 Conference Room
  alexsodt@gmail.com
  
  2/28 Dr. Zhong-Ru Xie (Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego)
  Ligand Docking and Structure-based Drug Design
  Time: 4:00 pm
  Location: MRB 200 Conference Room
  amianxie@gmail.com
  
  2/28 Dr. Alexej Abyzov (Department of Molecular Biophysics and Biochemistry, Yale University)
  Detecting Genomic Variations in Human Cells and Determining their Impact
  Time: 9:30 am
  Location: MRB 200 Conference Room
  abyzov@gersteinlab.org
  
  2/25 Dr. Dipak Barua (Center for Nonlinear Studies, Los Alamos National Laboratory)
  Investigation of the roles of Src family tyrosine kinases in immune response signaling and their redundancy: focus on B cell receptor signaling
  Time: 11:00 am
  Location: MRB 100C
  dbarua@lanl.gov
  
  2/13 Dr. Feng Yue (Department of Cellular and Molecular Medicine, UCSD School of Medicine)
  A map of the cis-regulatory sequences in the mouse genome
  Time: 3:30 pm
  Location: Haworth 1005
  fyue@ucsd.edu
  
  2/6 Dr. Christian Ray (Department of Systems Biology, The University of Texas M.D. Anderson Cancer Center)
  Toxic Assets in Cellular Economies
  Time: 2:00 pm
  Location: Haworth 1005
  jjray@mdanderson.org
  
  1/23 Dr. Hao Fan (Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco)
  Ligand discovery Guided by Homology Modeling and Docking: Application to Enzyme Function Annotation
  Time: 3:30 pm
  Location: Haworth 1005
  hfan@salilab.org
  
  
  

  2012 Fall Semester

  
  11/7 Dr. Jooyoung Lee (Center for In Silico Protein Science, Korea Institute for Advanced Study)
  Extracting hidden information from large-scale biological networks by optimal community detection
  Time: 2:00 pm
  Location: MRB 200 Conference Room
  jlee@kias.re.kr
  
  10/30 Dr. Thomas Cheatham (Department of Medicinal Chemistry, University of Utah)
  Moving from assessment and validation towards application to Hepatitis C virus IRES targeting
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  tec3@utah.edu
  
  10/23 Dr. David Weliky (Department of Chemistry, Michigan State University)
  Structure/function of membrane-associated viral fusion proteins and structure of recombinant proteins in bacterial inclusion bodies
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  weliky@chemistry.msu.edu
  
  
  

  2012 Summer Semester

  
  7/26 Afra Panahi (Department of Biochemistry & Molecular Biology, Michigan State University)
  Implicit solvent membrane with adaptive thickness
  Time: 10:00 am
  Location: MRB 200 Conference Room
  panahiaf@msu.edu
  
  
  

  2012 Spring Semester

  
  4/24 Dr. K. Jebrell Glover (Department of Chemistry, Lehigh University)
  Proteins as Architects of Cell Membranes: Probing the structure of caveolin-1
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  kjg206@lehigh.edu
  
  4/17 Dr. Marc Ostermeier (Department of Chemical and Biomolecular Engineering, Johns Hopkins University)
  Protein switches and bacterial band-pass filters
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  oster@jhu.edu
  
  3/5 Dr. Upadhyayula Surya Raghavender (SRI International)
  Conformationally Constrained Designed Peptides forming Nanotubes and β-hairpins
  Time: 11:00 am
  Location: MRB 200 Conference Room
  
  2/29 Dr. Yinghao Wu (Depart of Biochemistry and Molecular Biology, Columbia University)
  Multiscale studies of cadherin-mediated cell adhesion
  Time: 3:30 pm
  Location: Haworth 1005
  yw2286@columbia.edu
  
  2/16 Tatsiana Kirys (Center for Bioinformatics, University of Kansas)
  Side-chain conformational preferences upon protein-protein binding
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  nushki@mail.ru
  
  2/8 Dr. Sarath Chandra Janga (Institute for Genomic Biology Fellow, University of Illinois at Urbana-Champaige)
  Dynamic and evolutionary constraints imposed on transcriptional and post-transcriptional regulatory networks
  Time: 3:30 pm
  Location: Haworth 1005
  sarath@igb.uiuc.edu
  
  2/1 Dr. Jiang Zhu (National Institute of Allergy and Infectious Diseases)
  Computational Biology, Making Inroads Into AIDS Vaccine Development
  Time: 3:30 pm
  Location: Haworth 1005
  zhuj3@niaid.nih.gov
  
  
  

  2011 Fall Semester

  
  12/6 Dr. Lukas Tamm (University of Virginia, Molecular Physiology and Biological Physics)
  Structure, Function, and Antibiotic Resistance of the Outer Membrane of Pseudomonas Aeruginosa
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  lkt2e@virginia.edu
  
  12/5 Dr. Andrea Bazzoli
  A protein design algorithm combining free-energy minimization and alignment to a target sequence profile
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  
  11/21 Dr. Jeffrey Skolnick (Center for the Study of Systems Biology, Georgia Institute of Technology)
  Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
  Time: 3:30 pm
  Location: 1005 Haworth
  jeffrey.skolnick@biology.gatech.edu
  
  11/8 Dr. Francisca M. Marassi (Sanford Burnham Research Institute)
  Structural studies of Membrane Proteins in Phospholipid Bilayers
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  fmarassi@sanfordburnham.org
  
  10/25 Dr. Wei Yang (Department of Chemistry and Biochemistry, Florida State University)
  The orthogonal space sampling towards the enabling of practically robust and effecient computational tools
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  yyang2@fsu.edu
  
  9/27 Dr. John Koh (Department of Chemistry and Biochemistry, University of Delaware)
  Chemical Rescue of Nuclear Receptors and Exploration of Next-Generation Antiandrogen
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  johnkoh@udel.edu
  
  9/13 Dr. Alexey Nesvizhskii (Center for Computational Medicine and Bioinformatics, University of Michigan Medical School)
  Computational methods for modeling AP/MS protein-protein interaction data
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  nesvi@med.umich.edu
  
  
  

  2011 Summer Semester

  
  7/6 Dr. Jooyoung Lee (Center for In Silico Protein Science & School of Computational Sciences, Korea Institute for Advanced Study)
  Global Optimization by Conformational Space Annealing and its Applications to Various Biological Systems
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  jlee@kias.re.kr
  
  
  

  2011 Spring Semester

  
  5/11 Dr. Ling Wu (University of Minnesota)
  Structural studies of Metalloproteinase and Protien-Ligand Binding systems
  Time: 11:00 am
  Location: MRB 200 Conference Room
  
  5/3 Dr. Rakwoo Chang (Department of Chemistry, Kwangwoon University)
  Recent Applications of Coarse-Grained Molecular Simulations in Biophysical Problems
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  
  4/28 Dr. Saugata Hazra (St. Jude Children's Research Hospital)
  Structure-Function Relationship of Human deoxycytidine kinase
  Time: 11:00 am
  Location: MRB 200 Conference Room
  
  4/18 Dr. Jian Dai (Department of Physics, Texas Tech University)
  A Comprehensive Study of Multi-Component Biomembranes Containing Cholesterol
  Time: 2:00 pm
  Location: MRB 200 Conference Room
  jian1.dai@ttu.edu
  
  4/5 Dr. David Volkin (Department of Pharmaceutical Chemistry, University of Kansas)
  Challenges and Opportunities to Better Characterize Higher-Order Protein Structure in Dosage Forms for Comparability Evaluations: Detecting Protein Aggregates/Particulates and Using Empirical Phase Diagrams
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  volkin@ku.edu
  
  3/18 Ayesha Khan
  Calibrating SCHEMA disruption for Adeno-Associated Virus Serotypes
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  
  3/15 Dr. Mark Fisher (Department of Biochemistry and Molecular Biology, University of Kansas Medical Center)
  Using the Chaperonin GroEL beyond Protein Folding
  Time: 2:00 pm
  Location: MRB 100 Conference Room
  mfisher1@kumc.edu
  
  2/15 Dr. Pengyu Ren (Department of Biomedical Engineering, The University of Texas at Austin)
  Molecular Modeling of Protein-Ligand Interactions
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  pren@mail.utexas.edu
  
  
  

  2010 Fall Semester

  
  12/6 Dr. Benoit Roux (Department of Biochemistry and Molecular Biology, University of Chicago)
  Computational study of the ligand-activated Glutamate Receptor
  Time: 3:30 pm
  Location: 1005 Haworth Hall
  roux@uchicago.edu
  
  11/30 Dr. Sandeep Patel (Department of Chemistry and Biochemistry, University of Delaware)
  Recent Progress in Development and Application of Non-Additive Interaction Models for Molecular Simulations of Biophysical and Physicochemical Systems
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  spatel@mail.chem.udel.edu
  
  10/26 Dr. Ford Ballantyne (Assistant Professor, Department of Ecology and Evolutionary Biology, University of Kansas)
  The roles cellular and sub-cellular "decisions" play in biogeochemical cycles
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  fb4@ku.edu
  
  10/12 Dr. Robert P. Hanzlik (Professor, Department of Medicinal Chemistry, University of Kansas)
  Reactive Metabolite Target Proteomics. What Are We Learning?
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  rhanzlik@ku.edu
  
  9/23 Dr. Kyle V. Camarda (Department of Chemical and Petroleum Engineering, University of Kansas)
  Applications of Computational Molecular Design
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  camarda@ku.edu
  
  9/9 Dr. A. Keith Dunker (Department of Biochemistry and Molecular Biology, Indiana University School of Medicine)
  Bioinformatics and Intrinsically Disordered Proteins (IDPs)
  Time: 2:00 pm
  Location: MRB 200 Conference Room
  kedunker@iupui.edu
  
  9/7 Dr. Xiaoqin Zou (Assistant Professor of Biophysics and Bioinformatics, University of Missouri-Columbia)
  A new scoring framework for selecting structural models
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  zoux@missouri.edu
  
  
  

  2010 Spring Semester

  
  4/21 Dr. Mallika Veeramalai (Sanford-Burnham Medical Research Institute)
  Rapid database search for similar and flexible protein structures based on TOPS++FATCAT method
  Time: 10:00 am
  Location: MRB 200 Conference Room
  mallikav@burnham.org
  
  4/6 Dr. Marcella McClure (Dept of Microbiology and Center for Computational Biology, Montana State University)
  A Bioinformatic Approach to the Structure, Function, and Evolution of The Nucleoprotein Of The Order Mononegavirales
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  marsmcclure@gmail.com
  
  3/24 Dr. Mihaela Sardiu (Stowers Institute for Medical Research)
  Towards a comprehensive understanding of protein networks underlying chromatin remodeling complexes
  Time: 11:00 am
  Location: MRB 200 Conference Room
  MIS@stowers.org
  
  3/11 Dr. Yan Yuan Tseng (University of Chicago)
  A geometric approach to protein structure, function and evolution
  Time: 11:00 am
  Location: MRB 100 Conference Room
  ytseng3@uchicago.edu
  
  3/8 Dr. Eric Deeds (Harvard Medical School)
  The Dynamics of Assembly in Biological Networks
  Time: 11:00 am
  Location: MRB 200 Conference Room
  deeds@hms.harvard.edu
  
  3/1 Dr. Remo Rohs (Howard Hughes Medical Institute, Columbia University)
  The Role of DNA Shape in Protein-DNA Recognition
  Time: 11:00 am
  Location: MRB 200 Conference Room
  rr2213@columbia.edu
  
  
  

  2009 Fall Semester

  
  12/1 Dr. Eric Walters (Professor, Department of Biochemistry & Molecular Biology, Rosalind Franklin University of Medicine and Science, IL)
  Virtually Everything You Wanted to Know about Citrate Transport: Computer Modeling Studies of a Membrane Protein
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  eric.walters@rosalindfranklin.edu
  
  11/24 Dr. David Eliezer (Department of Biochemistry, Weill Medical College of Cornell University)
  Structure Transitions of the Parkinson's and Alzheimer's linked proteins synuclein and tau
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  eliezer@med.cornell.edu
  
  11/17 Dr. Ying Xu (Director, Institute of Bioinformatics, University of Georgia)
  Elucidation of Rules that Govern the Genomic Structures of Bacteria
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  xyn@bmb.uga.edu
  
  11/10 Dr. David A. Liberles (Department of Molecular Biology, University of Wyoming)
  Understanding the Lineage-Specific Amino Acid Substitution Process
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  liberles@uwyo.edu
  
  11/9 Dr. Yuji Sugita (Theoretical Biochemistry Laboratory, RIKEN)
  The generalized-ensemble simulations and its application to the protein folding problem
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  sugita@riken.jp
  
  11/3 Dr. Xiongwu Wu (Laboratory of Computational Biology, National Heart Lung and Blood Institute, NIH)
  Electron tomography and molecular modeling study of chemoreceptor organization
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  wuxw@nhlbi.nih.gov
  
  10/20 Dr. Toshi Hoshi (Department of Physiology, University of Pennsylvania)
  Activation of the large-conductance Ca2+- and voltage-gated Slo1 K+ channel by Ca2+, H+ and carbon monoxide
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  hoshi@mail.med.upenn.edu
  
  10/13 Dr. Richard Pastor (Laboratory of Computational Biology, National Heart Lung and Blood Institute, NIH)
  Computer Simulations of NMR Relaxation in Lipid Bilayers
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  pastorr@nhlbi.nih.gov
  
  9/22 Dr. Olaf S. Andersen (Department of Physiology and Biophysics, Weill Medical College of Cornell University)
  Lipid bilayers as regulators of membrane protein function
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  sparre@med.cornell.edu
  
  8/28 Dr. Feng Chen (Kansas State University)
  Development and testing of protein backbone torsional potentials for the Kirkwood Buff derived force field of peptides and proteins
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  chenfeng112@hotmail.com
  
  8/27 Dr. Yogita Mantri (University of Indiana)
  Computational Modeling of Transition Metals in Medicinal Chemistry: Modeling the Copper-bound Amyloid-β peptide of Alzheimer’s Disease
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  ymantri@indiana.edu
  
  

  2009 Summer Semester

  
  7/7 Dr. Yongqun He (Department of Microbiology and Immunology, University of Michigan Medical School)
  Vaccine Informatics for Vaccine Research and Development
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  yongqunh@med.umich.edu
  
  

  2009 Spring Semester

  
  5/12 Dr. Sarah Hymowitz (Senior Scientist: Structural Biology, Genentech)
  Structural biology of therapeutic targets in the TNF receptor superfamily
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  
  5/6 Dr. Stas Shvartsman (Associate Professor of Chemical Engineering and the Lewis Sigler Institute for Integrative Genomics, Princeton University)
  MAPK signaling in equations and embryos
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  stas@princeton.edu
  
  5/1 Stephen O. Opiyo (School of Biological Sciences, University of Nebraska-Lincoln, Nebraska)
  Mining G-protein coupled receptors from plant genomes
  Time: 11:00 am
  Location: MRB 200 Conference Room
  opiyo@unlserve.unl.edu
  
  4/28 Dr. Themis Lazaridis (Chemistry Department, City College of New York)
  Modeling protein-membrane interactions using implicit solvation
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  tlazaridis@sci.ccny.cuny.edu
  
  4/14 Dr. Stanley Opella (Department of Chemistry and Biochemistry, University of California, San Diego)
  Towards an Integrated View of the Structure and Dynamics of Membrane Proteins
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  sopella@ucsd.edu
  
  4/7 Dr. Anthony Kossiakoff (Department of Biochemistry & Molecular Biology, University of Chicago)
  Synthetic antibodies evolved from a minimal genetic code and their applications to structural and cell biology.
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  koss@bsd.uchicago.edu
  
  3/31 Dr. Roger E. Koeppe II (Department of Chemistry and Biochemistry, University of Arkansas)
  Perspectives on arginine and proline in membrane-spanning peptides
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  rk2@uark.edu
  
  3/24 Dr. Wolfgang Peti (Department of Molecular Pharmacology, Physiology & Biotechnology, Brown University)
  Structural Basis of Protein Phosphatase 1 Regulation
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  Wolfgang_Peti@brown.edu
  
  3/3 Dr. Robert Dunn (Department of Chemistry, University of Kansas)
  Probing Biological Function at the Single Molecule Level
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  rdunn@ku.edu
  
  3/2 PhD Candidates
  Time: 9:30 - 11 am
  Location: MRB 100 Conference Room
  9:30: Michael Rowland
  Complement 1s is the serine protease that cleaves IGFBP-5 in human osteoarthritic joint fluid
  10:00: Parul V. Kudtarkar
  Roundup: Scaling computation to compute orthologs
  10:30: Xianghong Qi
  INFLUENCE OF COOPERATIVITY ON THE PROTEIN FOLDING MECHANISM
  
  2/24 Dr. Moosa Mohammadi (NYU Langone Medical Center)
  Molecular Mechanisms of FGF Receptor Regulation in Development and its Corruption in Disease
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  Moosa.Mohammadi@nyumc.org
  
  2/17 Dr. Mario Rivera (University of Kansas)
  Toward a molecular understanding of iron acquisition and homeostasis in Pseudomonas aeruginosa
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  mrivera@ku.edu
  
  2/10 Dr. Heather Desaire (University of Kansas)
  Glycoprotein Analysis for HIV Vaccine Development
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  hdesaire@ku.edu
  
  2/3 Dr. Dong Xu (Computer Science Department, University of Missouri)
  MUFOLD: A New Protein Structure Prediction System
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  xudong@missouri.edu
  
  

  2008 Fall Semester

  
  12/9 Dr. Mark Walter (Department of Microbiology, University of Alabama at Birmingham)
  Protein Design by Virus
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  walter@cbse.uab.edu
  
  12/2 Dr. Joan-Emma Shea (Department of Chemistry and Biochemistry, Department of Physics, University of California, Santa Barbara)
  Simulations of protein aggregation
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  shea@chem.ucsb.edu
  
  11/18 Dr. Robert Stroud (Professor of Biochemistry & Biophysics, Professor of Pharmaceutical Chemistry, University of California San Francisco)
  Regulating ammonia and water transport across membranes; QED!
  Time: 1:00 pm
  Location: MRB 100 Conference Room
  stroud@msg.ucsf.edu
  
  11/11 Dr. Ron Elber (Professor of Chemistry and Biochemistry and W.A. "Tex" Moncrief Chair in Computational Life Sciences and Biology, University of Texas)
  Sequence networks, capacity, and flow between protein structures
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  ron@ices.utexas.edu
  
  11/4 Dr. Kwang Hun Lim (Chemistry, East Carolina University)
  NMR Studies of Protein Misfolding and Amyloid Formation
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  limk@ecu.edu
  
  10/28 Dr. Liang Tang (Department of Molecular Biosciences, University of Kansas)
  Assembly of large dsDNA viruses
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  tangl@ku.edu
  
  10/14 Dr. Roberto De Guzman (Department of Molecular Biosciences, University of Kansas)
  NMR studies of bacterial and viral pathogenesis
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  rdguzman@ku.edu
  
  10/7 Dr. Andrew Neuwald (Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine )
  The charge-dipole pocket: a Ras-like GTPase component associated with switch II restructuring
  Time: 1:00 pm
  Location: MRB 200 Conference Room
  aneuwald@som.umaryland.edu
  
  9/30 Dr. Jeffrey Klauda (Department of Chemical and Biomolecular Engineering, University of Maryland)
  Structure and Dynamics of Lipids, Model Cellular Membranes, and Membrane Proteins
  Time: 11:00 am
  Location: MRB 200 Conference Room
  jbklauda@umd.edu
  
  9/23 Dr. Scott Feller (Department of Chemistry, Wabash College)
  Unique properties of omega-3 fatty acids: implications for rhodopsin function
  Time: 11:00 am
  Location: MRB 200 Conference Room
  fellers@wabash.edu
  
  9/16 Dr. Wonpil Im (University of Kansas Center for Bioinformatics)
  Insertion, folding, tilting, and assembly of transmembrane helices
  Time: 11:00 am
  Location: MRB 200 Conference Room
  wonpil@ku.edu
  
  9/9 Dr. Sitao Wu (Zhang Lab, University of Kansas Center for Bioinformatics)
  Sequence-based protein contact prediction and its usage in 3D protein structure modeling
  Time: 11:00 am
  Location: MRB 200 Conference Room
  stwu@ku.edu
  
  9/2 Dr. Shiyong Liu (Vakser Lab, University of Kansas Center for Bioinformatics)
  Scoring function on protein-protein docking
  Time: 11:00 am
  Location: MRB 200 Conference Room
  syliu@ku.edu
  
  

  2008 Spring Semester

  
  5/20 Dr. Eugene Krissinel (Senior Technical Officer, European Bioinformatics Institute)
  PISA, or a story about perceptions, expectations, naivety, macromolecular complexes and their complexity in bioinformatics and crystallography
  Time: 11:00 am
  Location: MRB 200 Conference Room
  keb@ebi.ac.uk
  
  5/6 Dr. Jie Liang (Department of Bioengineering, University of Illinois at Chicago)
  Detecting geometric pattern and evolutionary signal from protein structure for understanding biological functions and predicting protein-protein interaction surfaces
  Time: 11:00 am
  Location: MRB 200 Conference Room
  jliang@uic.edu
  
  4/29 Dr. Alexander Tropsha (Professor and Chair, The Laboratory for Molecular Modeling, Division for Medicinal Chemistry & Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill)
  Protein Comparison: From New Methods to Unexpected Discoveries
  Time: 11:00 am
  Location: MRB 200 Conference Room
  alex_tropsha@unc.edu
  
  4/22 Dr. Nick Grishin (Department of Biochemistry, University of Texas Southwestern Medical Center)
  Protein Comparison: From New Methods to Unexpected Discoveries
  Time: 11:00 am
  Location: MRB 200 Conference Room
  grishin@chop.swmed.edu
  
  4/8 Dr. Michael Gilson (Center for Advanced Research in Biotechnology, University of Maryland)
  Entropy, Affinity and the Design of Targeted Molecules
  Time: 11:00 am
  Location: MRB 200 Conference Room
  gilson@umbi.umd.edu
  
  3/13 Dr. Scott Christley (Department of Computer Science and Engineering, University of Notre Dame)
  Vertebrate Limb Chondrogenesis and Invertebrate Comparative Genomics
  Time: 2:00 - 3:15 pm
  Location: Nichols Hall Apollo Room
  schristl@nd.edu
  
  3/11 Dr. Zhi Wei (Genomics and Comp. Bio. Graduate Group, Univ. of Penn. School of Medicine)
  Markov Random Field Models for Network-Based Analysis of Genomic Data
  Time: 2:00 - 3:15 pm
  Location: Nichols Hall Apollo Room
  zhiwei04@gmail.com
  
  2/20 Dr. Phillip Bourne (University of California, San Diego)
  What Does Evolution Tell Us About Drug Discovery?
  Time: 1:30 pm
  Location: MRB 200 Conference Room
  bourne@ucsd.edu
  
  2/5 Petras Kundrotas (University of Kansas)
  Sequence-homology based approach in modeling of protein-protein interactions
  Time: 11:00 am
  Location: MRB 200 Conference Room
  pkundro@ku.edu
  
  1/31 Iddo Friedberg (University of California, San Diego)
  New Challenges for Structural Bioinformatics: Towards a Better Understanding of Structure and Function Space
  Time: 2:30 pm
  Location: 2023 Haworth
  idoerg@gmail.com
  
  1/29 Dr. Jeffry D Madura (Duquesne University)
  Simulations of LeuT and DAT Transporters
  Time: 11:00 am
  Location: MRB 200 Conference Room
  madura@duq.edu
  
  1/24 John Karanicolas (University of Washington)
  Design of de novo protein-protein interfaces
  Time: 2:30 pm
  Location: 2023 Haworth
  johnk4@u.washington.edu
  
  1/17 Natarajan Kannan (University of California, San Diego)
  Evolutionary Clues to Protein Kinase Regulatory Mechanisms
  Time: 2:30 pm
  Location: 2023 Haworth
  
  

  2007 Fall Semester

  
  12/11 Dr. Jooyong Lee (Korea Institute for Advanced Study)
  High Accuracy Protein Structure Prediction by Global Optimization
  Time: 11:00 am
  Location: MRB 200 Conference Room
  jlee@kias.re.kr
  
  11/13 Dr. Nathan Baker (Washington University in St. Louis)
  Assessing the performance of Poisson-Boltzmann continuum solvation models
  Time: 11:00 am
  Location: MRB 200 Conference Room
  baker@ccb.wustl.edu
  
  10/30 Dr. Qiang Cui (The University of Wisconsin-Madison)
  Mechanochemical coupling in Molecular Motors: insights from molecular simulations at multiple scales
  Time: 11:00 am
  Location: MRB 200 Conference Room
  cui@chem.wisc.edu
  
  10/23 Dr. Arcady Mushegian (The University of Kansas School of Medicine, Stowers Institute for Medical Research)
  Evolutionary history of bacteriophages with double-stranded DNA genomes
  Time: 11:00 am
  Location: MRB 200 Conference Room
  arm@stowers-institute.org
  
  10/09 Dr. Ram Samudrala (University of Washington)
  Modeling Interactomes
  Time: 2:00 pm
  Location: MRB 200
  ram@compbio.washington.edu
  
  09/25 Dr. Krzysztof Kuczera (University of Kansas)
  Domain motions in a tetrameric enzyme: modeling and experimental studies
  Time: 2:00 pm
  Location: MRB Conference Room
  kkuczera@ku.edu
  
  09/18 Dr. Jianwen Fang (University of Kansas)
  Bioinformatics of Polyanion Binding Proteins
  Time: 2:00 pm
  Location: MRB Conference Room
  jwfang@ku.edu
  
  8/23 Dr. Marta Sales (Northwestern University)
  Topology and Dynamics of Complex Biological Systems
  Time: 11:00
  Location: MRB 200
  msales@northwestern.edu
  
  8/7 Dr. Petras Kundrotas (Clemson University)
  Predicting 3D structure of protein-protein complexes
  Time: 11:00
  Location: MRB 200
  pkundro@clemson.edu
  
  

  2007 Spring Semester

  
  1/11 Leonor Saiz (Computational Biology Center at Memorial Sloan-Kettering Cancer Center, New York, NY)
  Multilevel Modeling of Biological Processes: From Molecular Interactions at the Cell Membrane to the Dynamics of Gene Regulation Networks
  Time: 2:00
  Location: Haworth Room 2031
  leonor@cbio.mskcc.org
  
  1/17 Maricel Kann (NIH/NLM/NCBI)
  Bioinformatics of protein domains: new computational approaches for the detection of protein domains and their interactions
  Time: 2:00
  Location: Haworth Room 2023
  kann@ncbi.nlm.nih.gov
  
  1/25 Min-yi Shen (Dept of Biopharmaceutical Sciences, UCSF)
  High-Accuracy Modeling of Protein Structures
  Time: 11:00
  Location: MRB 100C
  smy@salilab.org
  
  2/13 Shailesh Date (Dept. of Genetics, University of Pennsylvania School of Medicine)
  Computational modeling of interactomes: Tools, techniques and application to genomes of apicomplexan parasites
  Time: 11:00
  Location: 2001 Mallott
  svdate@pcbi.upenn.edu
  
  2/15 Huiying Li (UCLA-DOE Institute for Genomics and Proteomics)
  From genome to gene expression: Understanding protein interactions and host-pathogen interactions
  Time: 12:00
  Location: 2001 Mallott
  huiying@mbi.ucla.edu
  
  2/22 Ester Lo (The University of Tulsa)
  Influence of Meteorological Conditions on Early Spring Pollen in the Tulsa Atmosphere from 1987 to 2006
  Time: 11:00
  Location: MRB Conference Room
  esther-lo@utulsa.edu
  
  2/22 Craig Helstowski (The University of Connecticut)
  Profiling Phylogenetic Informativeness in Angiosperms Amborella and Nymphaeales
  Time: 11:45
  Location: MRB Conference Room
  craig.helstowski@uconn.edu
  
  2/22 Dr. David Mobley (University of California San Francisco)
  Challenges in predicting ligand binding free energies in a model binding site
  Time: 3:00
  Location: 2100 Mallott
  dmobley@gmail.com
  
  3/7 Dr. Jimin Pei (University of Texas Southwestern Medical Center)
  Challenges in predicting ligand binding free energies in a model binding site
  Time: 2:00
  Location: 2100 Mallott
  jpei@chop.swmed.edu
  
  4/24 Toby Allen (University of California, Davis)
  The energetics of arginine-lipid interactions with implications for ion channel gating
  Time: 3:00
  Location: MRB Conference Room
  twallen@ucdavis.edu
  
  5/01 Ioan Andricioaei (University of Michigan)
  On the Force Dependence of Biomolecular Conformational Kinetics
  Time: 11:00
  Location: MRB Conference Room
  andricio@umich.edu
  
  

  2006 Fall Semester

  Time: 3:00
  Place: Conference Room at Center for Bioinformatics (200 MRB)
  
  9/5 Shiyong Liu (Vakser lab)
  Protein-protein interface recognition and design
  Note: time for only this seminar is 2:30
  liushiyong@gmail.com
  
  9/12 Jagtar Hunjan (Vakser lab)
  Probing energy funnel in transient protein complexes
  jagtar@ku.edu
  
  9/19 Sitao Wu (Zhang Lab)
  Ab initio modeling of small proteins by iterative TASSER simulations
  stwu@ku.edu
  
  9/26 Ruvinsky/Vakser (Vakser lab)
  Analysis of intermolecular energy landscape in protein-protein interactions
  ruvinsky@ku.edu
  
  10/3 Thenmalar Ratinavelan (Im lab)
  Towards de novo structure determination of biomacromolecules using
  solely residual dipolar coupling
  thenmcr@ku.edu
  
  10/10 Zhengwei Zhu (Vakser lab)
  GWIDD: A Genome-wide Docking Database
  zzhu@ku.edu
  
  10/17 Luke Huan (EECS)
  Graph-based pattern discovery in protein structures
  jhuan@eecs.ku.edu
  
  10/24 No seminar
  
  10/31 Andrey Tovchigrechko (Vakser lab)
  Adapting intermolecular potentials to FFT correlation search
  andrey@ku.edu
  
  11/7 Stephan Lorenzen (Zhang Lab)
  Refinement of docking decoys by Monte Carlo methods
  stephlo@ku.edu
  
  11/14 Ying Gao (Vakser lab)
  Database of Unbound structures from Protein-Protein
  Co-crystal Structures
  ygao1@ku.edu
  
  11/21 - no seminar
  
  11/28 Jinhyuk Lee (Im lab)
  Helix-helix restraint potentials
  jinhyuk@ku.edu
  
  12/14 Wenjun Zheng (NHLBI, National Institutes of Health, Bethesda, MD)
  Decrypting conformational dynamics in myosin motor with a coarse-grained elastic model
  Time: 1:00
  Location: Haworth Room 2031
  
  

  2006 Spring Semester

  • January 26, Thu
    4:00pm - 5:00pm, 6031 Haworth
    Nilesh Banavali
    Weill Medical College of Cornell Univesity, NY
    Understanding Conformational Changes using Molecular Dynamics
  • February 2, Thu
    3:30pm - 4:30pm, 1001 Malott
    Margaret Shun Cheung
    Institute for Physical Science and Technology, University of Maryland
    Life in a Crowd: Macromolecular Crowding and Confinement Effects on Protein Interactions in Living Systems
  • February 6, Mon
    3:30pm - 4:30pm, 1001 Malott
    Jianhan Chen
    Department of Molecular Biology, The Scripps Research Institute, CA
    Folding Proteins from First-Principles
  • February 9, Thu
    3:30pm - 4:30pm, 1001 Malott
    Sandeep Patel
    Department of Molecular Biology, The Scripps Research Institute, CA
    Development and Applications of Polarizable Force Fields for Molecular Dynamics Simulations of Biological Molecules
  • February 15, Wed
    3:30pm - 4:30pm, 1005 Malott
    Gunasekaran Kannan
    National Cancer Institute-NIH, MD
    Conformational Flexibility and Function in Intrinsically Disordered and Ordered Proteins
  • February 20, Mon
    3:30pm - 4:30pm, 6031 Haworth
    Gennady Verkhivker
    University of California at San Diego
    Integrating bioinformatics, protein modeling and computational chemical genomics approaches in predicting protein kinases structure and binding with ligands and interacting proteins: Towards understanding the molecular basis of human disease and in silico drug discovery
  • April 28, Fri
    3:00pm - 4:30pm, 1005 Haworth
    Alex MacKerell
    University of Maryland
    Structure-function relationships of nucleic acids and protein-nucleic acid complexes studied via MD simulations

  2005 Fall Semester

  • August 31, Wed
    11:00am - 12:00am, Pine Room, Kansas Union
    James Lu
    Lawrence Berkeley National Lab, Berkeley, CA
    When Visual Simulation meets Computational Biology
  • September 21, Wed
    10:00am - 11:00am, Pine Room, Kansas Union
    Ping Yang
    Michigan Technological University
    Intramolecular Hydrogen Bonding Network in myo-inositol phosphates and Surface Passivation of Quantum Dots
  • November 11, Fri
    3:30pm - 4:30pm, Alcove F, Level 3 of the Kansas Union
    Matthew Miller
    University of Missouri, Kansas City
    Quantum Mechanical Methods for Prediction of Thermodynamic Properties and QSAR Modeling
  • November 23, Wed
    9:00am - 10:00am, International Room, Kansas Union
    Alexander Rubinstein
    Eppley Institute for Research in Cancer and Allied Diseases and Department of Pharmaceutical Science, College of Pharmacy, University of Nebraska Medical Center, Omaha
    Non-local electrostatic effects at the protein-solvent interface within macroscopic continuum model
  • December 2, Fri
    10:00am - 11:00am, Regionalist Room, Kansas Union
    Dennis Law
    San Diego Supercomputer Center, CA
    Combining Experimental Information and Computational Methods to Produce Testable Models for Protein Complexes
  • December 22, Thu
    11:00am - 12:0pm, International Room, Kansas Union
    Anatoly Ruvinsky
    Center for Bioinformatics, The University of Kansas
    A novel statistical-thermodynamic method for computation of the protein-ligand association entropy: the profound consequences for docking accuracy

  2005 Spring Semester

  • May 4, Wed
    1:30pm - 2:30pm, Apollo Room, Nichols Hall
    Daniel Fischer
    University of Buffalo
    Unraveling the puzzle of genomic ORFans
  • May 23, Mon
    4:00pm - 5:00pm, rm 1005, Haworth Hall
    Hui Lu
    University of Illinois Chicago
    Structural Bioinformatics Prediction of Protein-DNA interactions
  • June 21, Tue
    10:00am - 11:00am, rm 2046, Haworth Hall
    Vitaly Khutorsky
    Larial Proteomics Inc., Toronto
    Structure Activity Relationships (SAR) of Membrane Bound Compounds and Complexes
  • June 22, Wed
    10:00am - 11:00am, rm 2046, Haworth Hall
    Ying Gao
    Purdue University, Indiana
    Protein-protein interfaces and drug design